sequenceDesignMatrix: Create design matrix for sequences
In benilton/oligo-release: Preprocessing tools for oligonucleotide arrays.

Description Usage Arguments Details Value Examples

Creates design matrix for sequences.

1	sequenceDesignMatrix(seqs)

seqs

character vector of 25-mers.

This assumes all sequences are 25bp long.

The design matrix is often used when the objecive is to adjust intensities by sequence.

Matrix with length(seqs) rows and 75 columns.

genSequence <- function(x)
    paste(sample(c("A", "T", "C", "G"), 25, rep=TRUE), collapse="", sep="")
seqs <- sapply(1:10, genSequence)
X <- sequenceDesignMatrix(seqs)
Y <- rnorm(10, mean=12, sd=2)
Ydemean <- Y-mean(Y)
X[1:10, 1:3]
fit <- lm(Ydemean~X)
coef(fit)